X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 30% JEFFAMINE M-600, MES PH 6.5, 50 MM CSCL

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.39 α = 90
b = 108.39 β = 90
c = 102.81 γ = 120
Symmetry
Space Group P 62

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH MIRRORS 2001-05-15
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 -- ESRF ID29

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.5 27 97.3 0.071 -- -- 5.2 -- 23044 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.5 2.59 84.6 0.421 -- 1.9 3.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MAD 2.4 33.52 -- -- -- 25316 1281 100.0 -- -- 0.201 0.276 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.4 2.46 -- 94 1845 0.235 0.324 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.38
Anisotropic B[1][1] -3.11
Anisotropic B[1][2] -1.55
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.67
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.914
r_scbond_it 3.493
r_mcangle_it 2.251
r_mcbond_it 1.249
r_nbd_refined 0.4
r_gen_planes_refined 0.012
r_chiral_restr 0.171
r_dihedral_angle_3_deg 21.398
r_dihedral_angle_1_deg 5.322
r_angle_refined_deg 2.675
r_bond_refined_d 0.028
r_xyhbond_nbd_refined 0.22
r_metal_ion_refined 0.155
r_symmetry_hbond_refined 0.676
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3793
Nucleic Acid Atoms 0
Heterogen Atoms 688
Solvent Atoms 151

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.0.36 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0.36 refinement
SHARP model building